"I am grateful that I was able to help move CNE forward in homeownership promotion and preservation, and in the revitalization of urban neighborhoods," Johnson said.

But former employees alleged and a city audit confirmed that there were "very serious" financial discrepancies under Johnson.

The organization failed to secure permits or get inspections for some of its work, didn't provide evidence that it had properly procured contractors and didn't provide evidence that work had actually been completed, according to an audit.

The Times Free Press reported in September allegations that CNE paid kickbacks to contractors with taxpayer dollars and retaliated against whistleblowers.

Johnson also came under fire that month from a group of former workers who alleged that he engaged in sexual and racial discrimination, primarily against female and black employees.

Johnson, who is black, declined to comment. Officials said that his departure today was a retirement, not a forced resignation.

"CNE worked quickly to execute the program, helping more than 650 struggling homeowners in Chattanooga and Hamilton County combat rising utility costs through a variety of weatherproofing techniques," Littlefield said.